Limitations¶

This document explicitly lists what perfusio does not model or support.

Out-of-Scope Biology¶

Critical Quality Attributes (CQAs) — No modelling of glycoforms, charge variants, aggregates, HCP, or other product quality attributes. The model tracks titer (mg/L) only.
Medium composition — The medium formulation is hard-coded to a generic CHO basal medium. Proprietary feed and basal media are not supported.
Cell line specifics — Only two virtual cell lines (CloneX, CloneY) are provided. Real cell-line parameters require calibration.
3D fluid dynamics — The model is zero-dimensional (perfectly mixed). Spatial gradients in ambr®250 microbioreactors are not captured.
Viral clearance — No modelling of virus removal steps or biosafety considerations.

Dissolved oxygen control — DO is tracked as a state variable but control (sparge rate, agitation) is not modelled.
pH control — pH is not a state variable in this implementation.
Temperature ramping — Temperature is a fixed parameter; dynamic temperature shift protocols are not supported.
Fed-batch mode — The model assumes continuous perfusion; fed-batch and perfusion-start transitions are not implemented.

GMP validation — perfusio is not validated under 21 CFR Part 11, EU Annex 11, or any GxP framework. See docs/source/regulatory-considerations.md.
Electronic signatures — AuditLogger produces audit records but not compliant electronic signatures.
CSV injection — The FilesystemStore does not sanitise CSV fields for spreadsheet-formula injection; do not open output CSVs in untrusted spreadsheet applications.

Wall-clock speed — Training 27 Box-Behnken runs × 28 days on CPU takes approximately 2–5 minutes. GPU acceleration is available but not CI-tested.
Scalability — The SQL schema and SQLite backend are not intended for multi-site or high-throughput deployments (> 100 concurrent reactors).